Class: Thermostat¶

Settings used for the simulation thermostat.

URI: https://CCPBioSim.ac.uk/biosim-schema/Thermostat

         classDiagram
    class Thermostat
    click Thermostat href "../../classes/Thermostat/"
      Thermostat : chain_length
        
      Thermostat : collision_frequency
        
          
    
        
        
        Thermostat --> "0..1" FrequencyQuantity : collision_frequency
        click FrequencyQuantity href "../../classes/FrequencyQuantity/"
    

        
      Thermostat : coupling_group
        
      Thermostat : friction_coefficient
        
          
    
        
        
        Thermostat --> "0..1" FrictionCoefficientQuantity : friction_coefficient
        click FrictionCoefficientQuantity href "../../classes/FrictionCoefficientQuantity/"
    

        
      Thermostat : target_temperature
        
          
    
        
        
        Thermostat --> "0..1" TemperatureQuantity : target_temperature
        click TemperatureQuantity href "../../classes/TemperatureQuantity/"
    

        
      Thermostat : target_temperature_vector
        
          
    
        
        
        Thermostat --> "0..1" VectorTemperatureQuantity : target_temperature_vector
        click VectorTemperatureQuantity href "../../classes/VectorTemperatureQuantity/"
    

        
      Thermostat : temperature_time_constant
        
          
    
        
        
        Thermostat --> "0..1" VectorTimeQuantity : temperature_time_constant
        click VectorTimeQuantity href "../../classes/VectorTimeQuantity/"
    

        
      Thermostat : thermostat_algorithm
        
          
    
        
        
        Thermostat --> "0..1" ThermostatAlgorithm : thermostat_algorithm
        click ThermostatAlgorithm href "../../enums/ThermostatAlgorithm/"

Slots¶

Name	Cardinality and Range	Description	Inheritance
thermostat_algorithm	0..1 ThermostatAlgorithm	List of thermostat algorithms used in the simulation	direct
target_temperature	0..1 TemperatureQuantity	Target/reference temperature set to reach in the simulation, given as a float	direct
target_temperature_vector	0..1 VectorTemperatureQuantity	Target/reference temperature set to reach in the simulation, given as a list …	direct
collision_frequency	0..1 FrequencyQuantity	Collision frequency for the integrator, given as a float	direct
temperature_time_constant	0..1 VectorTimeQuantity	Time constant for coupling the system temperature in seconds units, given as …	direct
coupling_group	0..1 string	A subset of atoms for which temperature is controlled, often needed for simul…	direct
chain_length	0..1 integer	Usually required in the Nosé-Hoover thermostat, the chain length (e	direct
friction_coefficient	0..1 FrictionCoefficientQuantity	Usually used in the Langevin thermostat, the friction coefficient determines …	direct

Usages¶

used by	used in	type	used
SimulationSettings	thermostat	range	Thermostat

Identifier and Mapping Information¶

Schema Source¶

from schema: https://CCPBioSim.ac.uk/biosim-schema/

Mappings¶

Mapping Type	Mapped Value
self	https://CCPBioSim.ac.uk/biosim-schema/Thermostat
native	https://CCPBioSim.ac.uk/biosim-schema/Thermostat

LinkML Source¶

Direct¶

name: Thermostat
description: Settings used for the simulation thermostat.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- thermostat_algorithm
- target_temperature
- target_temperature_vector
- collision_frequency
- temperature_time_constant
- coupling_group
- chain_length
- friction_coefficient

Induced¶

name: Thermostat
description: Settings used for the simulation thermostat.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  thermostat_algorithm:
    name: thermostat_algorithm
    description: List of thermostat algorithms used in the simulation.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: ThermostatAlgorithm
  target_temperature:
    name: target_temperature
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: temp0
          unit: K
        - engine: lammps
          key: temp
          unit: K
    description: Target/reference temperature set to reach in the simulation, given
      as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: TemperatureQuantity
  target_temperature_vector:
    name: target_temperature_vector
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: ref-t
          unit: K
    description: Target/reference temperature set to reach in the simulation, given
      as a list (e.g. 300, 300).
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: VectorTemperatureQuantity
  collision_frequency:
    name: collision_frequency
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: gamma_ln
          unit: 1/ps
    description: Collision frequency for the integrator, given as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: FrequencyQuantity
  temperature_time_constant:
    name: temperature_time_constant
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: tau-t
          unit: ps
    description: Time constant for coupling the system temperature in seconds units,
      given as a list (e.g. 300, 300).
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: VectorTimeQuantity
  coupling_group:
    name: coupling_group
    description: A subset of atoms for which temperature is controlled, often needed
      for simulating complex systems (e.g., protein in water), used in gromacs, given
      as a string
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: string
  chain_length:
    name: chain_length
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: nhc_chain_length
        - engine: gromacs
          key: nh-chain-length
    description: Usually required in the Nosé-Hoover thermostat, the chain length
      (e.g., nh-chain-length in GROMACS) is used to maintain canonical distribution,
      given as an integer.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: integer
    minimum_value: 0
  friction_coefficient:
    name: friction_coefficient
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: bd-fric
          unit: a/ps
    description: Usually used in the Langevin thermostat, the friction coefficient
      determines the strength of coupling between a system and a heat bath, given
      as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Thermostat
    domain_of:
    - Thermostat
    range: FrictionCoefficientQuantity